Showing : DEseq • reset
1
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
4
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6
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330
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
10 weeks ago • updated 9 weeks ago s-rhussien • 0
1
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2
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245
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
3 months ago • updated 12 weeks ago jbnrodriguez • 0
1
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2
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190
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
3 months ago krawczyk.margarita • 0
0
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2
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214
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 3 months ago by 35k • written 3 months ago by • 0
0
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1
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149
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
6 months ago ayy2110 • 0
1
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2
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287
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metage problem with DESeq
DESeq metagene2 metagene
updated 8 months ago by ▴ 10 • written 9 months ago by ▴ 10
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3
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411
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 9 months ago by 35k • written 9 months ago by • 0
0
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5
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480
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 10 months ago by 35k • written 10 months ago by • 0
1
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12
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2.4k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 13 months ago by 35k • written 6.6 years ago by • 0
1
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2
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323
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DESeq Error (nbinomTest ())
Deseq nbinomTest
18 months ago canfield ▴ 10
0
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7
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298
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DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 18 months ago by 3.4k • written 18 months ago by • 0
2
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3
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517
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 20 months ago by 35k • written 20 months ago by ▴ 10
1
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2
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216
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 20 months ago by ★ 3.7k • written 20 months ago by • 0
3
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5
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354
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 20 months ago by 35k • written 20 months ago by ▴ 780
1
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9
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421
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 20 months ago by ★ 3.7k • written 20 months ago by • 0
0
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7
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388
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
22 months ago husainmanagori1998 • 0
0
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1
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386
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 2.0 years ago by 35k • written 2.0 years ago by ▴ 10
2
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3
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468
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 2.1 years ago by 35k • written 2.1 years ago by ▴ 150
4
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4
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1.1k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 2.3 years ago by ▴ 30 • written 2.4 years ago by • 0
1
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2
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357
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 2.4 years ago by 35k • written 2.4 years ago by • 0
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0
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383
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.4 years ago kentfung • 0
0
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9
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702
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
2.8 years ago ariel • 0
3
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12
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621
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
2.8 years ago ariel • 0
2
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3
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882
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 3.0 years ago by 35k • written 3.0 years ago by ▴ 10
0
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1
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418
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 3.1 years ago by 35k • written 3.1 years ago by • 0
0
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3
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541
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
3.2 years ago Ben ▴ 30
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7
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2.1k
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DESeq2 install problem
deseq
updated 3.2 years ago by 35k • written 3.2 years ago by • 0
4
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7
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1.7k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 3.2 years ago by 35k • written 3.2 years ago by • 0
0
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3
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501
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 3.2 years ago by 35k • written 3.2 years ago by ▴ 60
3
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5
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586
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Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
0
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7
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606
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
4
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1
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12k
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The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
3.3 years ago ansari.sarabio • 0
1
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5
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497
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
3
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7
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544
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
3.3 years ago blastzone.heimerdinger ▴ 10
0
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8
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935
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DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
0
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1
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395
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how to start normalization
deseq
3.4 years ago raghavaraghava049 • 0
0
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1
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425
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Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 3.4 years ago by 35k • written 3.4 years ago by • 0
0
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3
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437
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3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 3.4 years ago by 35k • written 3.4 years ago by ▴ 60
2
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3
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764
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ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 3.5 years ago by ★ 3.7k • written 3.5 years ago by • 0
0
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5
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630
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How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 3.6 years ago by 35k • written 3.6 years ago by • 0
3
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7
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1.1k
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novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 3.6 years ago by ★ 2.6k • written 3.6 years ago by ▴ 10
1
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2
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723
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Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
3.7 years ago blehtine • 0
1
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8
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1.4k
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DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
3.8 years ago • updated 3.7 years ago SPbeginner • 0
1
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3
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643
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DEseq2 sample imbalance
deseq
3.8 years ago • updated 3.7 years ago aishu.jp ▴ 20
0
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4
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12k
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Normalization by DEseq
Genetics Normalization DESeq Genetics Normalization DESeq
updated 3.8 years ago by • 0 • written 11.1 years ago by ▴ 20
0
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8
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1.8k
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Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
3.8 years ago Marina • 0
0
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4
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644
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Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
3.8 years ago Deepali • 0
0
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2
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2.3k
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Problem loading or running DESeq2
deseq could not find function
updated 3.8 years ago by 35k • written 3.8 years ago by • 0
5
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3
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2.5k
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DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
3.9 years ago kevin.kingsland ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESEQ2 Results log2fold and pvalue changes after removing genes by Bine ▴ 20
Thank you!
Comment: DESEQ2 Results log2fold and pvalue changes after removing genes by Bine ▴ 20
Thank you for clarifying.
Comment: Illumina Expression analysis from iDAT files by Đạt • 0
Dear Sean and Mike, I have same question as Sean asked. As I know, the beadarray package in R allow us the do the analysis from bead-level…
Answer: DESEQ2 Results log2fold and pvalue changes after removing genes by Michael Love 35k
Swbarnes is correct. The pvalue depends on the dispersion which borrows information across genes. Also the size factors could differ.
Answer: Question about DESeq2 statistical analysis by Michael Love 35k
For questions about interpreting designs and writing up results I recommend to work with a local statistician. I unfortunately only have ti…
Votes
Answer: DESEQ2 Results log2fold and pvalue changes after removing genes
Answer: DESEQ2 Results log2fold and pvalue changes after removing genes
Comment: DESEQ2 Results log2fold and pvalue changes after removing genes
Answer: dba.contrast in DiffBind
Answer: dba.contrast in DiffBind
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